Research workbench
Crystal structure of the eal domain of C-di-gmp specific phosphodiesterase yaha in complex with activating cofactor mg++
Analyse Crystal structure of the eal domain of C-di-gmp specific phosphodiesterase yaha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LYK
- Type
- protein
- Length
- 1,011 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic di-gmp phosphodiesterase yaha
- EC
- 3.1.4.-
- UniProt
- P21514
- Ligands
- HB0, MG
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclic di-gmp phosphodiesterase yaha (EC 3.1.4.-) | protein | 253 | 45% helix, 24% strand | P21514 |
| C | Cyclic di-gmp phosphodiesterase yaha (EC 3.1.4.-) | protein | 252 | 44% helix, 23% strand | P21514 |
| D | Cyclic di-gmp phosphodiesterase yaha (EC 3.1.4.-) | protein | 253 | 44% helix, 23% strand | P21514 |
Ligands and binding sites
- HB0 · trans-4-(hydroxymethyl)cyclohexanol · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.77 | 0.79 | 95 | empty |
| 2 | 444 | 0.66 | 0.79 | 41 | empty |
| 3 | 378 | 0.66 | 0.80 | 44 | empty |
| 4 | 354 | 0.64 | 0.79 | 37 | empty |
| 5 | 109 | 0.41 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1170 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1159 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 532 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 390 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4LYK · Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in… · the same entry in another collection · chain B against B, TM-score 1.00
- P21514 · AlphaFold monomer V2.0 prediction for cyclic di-gmp phosphodiesterase pdel (P21514) · a predicted model of the same protein · chain C against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P21514
- Elsewhere: RCSB PDB 4LYK · PDBe 4LYK · UniProt P21514
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